Cyanogenic glycosides are present in several economically important plant foods. Amygdalin, one of the most common cyanoglucoside, can be found abundantly in the seeds of apples, bitter almonds, apricots, peaches, various beans, cereals, cassava and sorghum. Amygdalin has been used for the treatment of cancer, it shows killing effects on cancer cells by release of cyanide. However, its effect on bone structure has not been investigated to date. Therefore, the objective of this study was to determine a possible effect of amygdalin application on femoral bone microstructure in adult rabbits. Four month old rabbits were randomly divided into two groups of three animals each. Rabbits from E group received amygdalin intramuscularly at a dose 0.6 mg.kg^-1 body weight (bw) (group E, n = 3) one time per day during 28 days. The second group of rabbits without amygdalin supplementation served as a control (group C, n = 3). After 28 days, histological structure of femoral bones in both groups of rabbits was analysed and compared. Rabbits from E group displayed different microstructure in middle part of the compact bone and near endosteal bone surface. For endosteal border, an absence of the primary vascular longitudinal bone tissue was typical. This part of the bone was formed by irregular Haversian and/or by dense Haversian bone tissues. In the middle part of substantia compacta, primary vascular longitudinal bone tissue was observed. Cortical bone thickness did not change between rabbits from E and C groups. However, rabbits from E group had a significantly lower values of primary osteons' vascular canals and secondary osteons as compared to the C group. On the other hand, all measured parameters of Haversian canals did not differ between rabbits from both groups. Our results demonstrate that intramuscular application of amygdalin at the dose used in our study affects femoral bone microstructure in rabbits.